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- EMDB-50909: Structure of carbon monoxide dehydrogenase/acetyl-CoA synthase (C... -

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Basic information

Entry
Database: EMDB / ID: EMD-50909
TitleStructure of carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) in complex with ferredoxin (Clostridium autoethanogenum)
Map dataFull map that is locally filtered using a local resolution map from cryosparc
Sample
  • Complex: Carbon monoxide dehydrogenase/acetyl-CoA synthase in complex with ferredoxin
    • Protein or peptide: CO-methylating acetyl-CoA synthase
    • Protein or peptide: Carbon monoxide dehydrogenase/acetyl-CoA synthase beta subunit
    • Protein or peptide: Ferredoxin
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: Fe(3)-Ni(1)-S(4) cluster
Keywordsanaerobic CO2 fixation / acetyl-CoA synthesis / metalloenzyme / Wood-Ljungdahl pathway. / OXIDOREDUCTASE
Function / homology
Function and homology information


CO-methylating acetyl-CoA synthase / CO-methylating acetyl-CoA synthase activity / anaerobic carbon-monoxide dehydrogenase activity / acetyl-CoA metabolic process / 4 iron, 4 sulfur cluster binding / electron transfer activity / metal ion binding
Similarity search - Function
: / Carbon monoxide dehydrogenase subunit alpha ,N-terminal / Carbon monoxide dehydrogenase subunit alpha N-terminal domain / CO dehydrogenase/acetyl-CoA synthase complex beta subunit / Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase, domain 3 superfamily / CO dehydrogenase/acetyl-CoA synthase complex beta subunit , C-terminal / CO dehydrogenase/acetyl-CoA synthase complex beta subunit / ACS/CODH beta subunit C-terminal / 7Fe ferredoxin / Prismane-like, alpha/beta-sandwich ...: / Carbon monoxide dehydrogenase subunit alpha ,N-terminal / Carbon monoxide dehydrogenase subunit alpha N-terminal domain / CO dehydrogenase/acetyl-CoA synthase complex beta subunit / Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase, domain 3 superfamily / CO dehydrogenase/acetyl-CoA synthase complex beta subunit , C-terminal / CO dehydrogenase/acetyl-CoA synthase complex beta subunit / ACS/CODH beta subunit C-terminal / 7Fe ferredoxin / Prismane-like, alpha/beta-sandwich / Prismane-like superfamily / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
Ferredoxin / CO-methylating acetyl-CoA synthase
Similarity search - Component
Biological speciesClostridium autoethanogenum DSM 10061 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.1 Å
AuthorsYin MD / Lemaire ON / Wagner T / Murphy BJ
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Science / Year: 2025
Title: Conformational dynamics of a multienzyme complex in anaerobic carbon fixation.
Authors: Max Dongsheng Yin / Olivier N Lemaire / José Guadalupe Rosas Jiménez / Mélissa Belhamri / Anna Shevchenko / Gerhard Hummer / Tristan Wagner / Bonnie J Murphy /
Abstract: In the ancient microbial Wood-Ljungdahl pathway, carbon dioxide (CO) is fixed in a multistep process that ends with acetyl-coenzyme A (acetyl-CoA) synthesis at the bifunctional carbon monoxide ...In the ancient microbial Wood-Ljungdahl pathway, carbon dioxide (CO) is fixed in a multistep process that ends with acetyl-coenzyme A (acetyl-CoA) synthesis at the bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase complex (CODH/ACS). In this work, we present structural snapshots of the CODH/ACS from the gas-converting acetogen , characterizing the molecular choreography of the overall reaction, including electron transfer to the CODH for CO reduction, methyl transfer from the corrinoid iron-sulfur protein (CoFeSP) partner to the ACS active site, and acetyl-CoA production. Unlike CODH, the multidomain ACS undergoes large conformational changes to form an internal connection to the CODH active site, accommodate the CoFeSP for methyl transfer, and protect the reaction intermediates. Altogether, the structures allow us to draw a detailed reaction mechanism of this enzyme, which is crucial for CO fixation in anaerobic organisms.
History
DepositionJul 6, 2024-
Header (metadata) releaseFeb 5, 2025-
Map releaseFeb 5, 2025-
UpdateFeb 12, 2025-
Current statusFeb 12, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50909.png

Downloads & links

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Map

FileDownload / File: emd_50909.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull map that is locally filtered using a local resolution map from cryosparc
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 560 pix.
= 490.56 Å		0.88 Å/pix.
x 560 pix.
= 490.56 Å		0.88 Å/pix.
x 560 pix.
= 490.56 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.876 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.213
Minimum - Maximum-3.036999 - 4.367411
Average (Standard dev.)0.00033917147 (±0.02498293)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 490.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50909_msk_1.map
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Additional map: non-sharpened full map

Fileemd_50909_additional_1.map
Annotationnon-sharpened full map
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Additional map: The local resolution map used for local filtering

Fileemd_50909_additional_2.map
AnnotationThe local resolution map used for local filtering
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Half map: #2

Fileemd_50909_half_map_1.map
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Half map: #1

Fileemd_50909_half_map_2.map
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Sample components

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Entire : Carbon monoxide dehydrogenase/acetyl-CoA synthase in complex with...

EntireName: Carbon monoxide dehydrogenase/acetyl-CoA synthase in complex with ferredoxin
Components
  • Complex: Carbon monoxide dehydrogenase/acetyl-CoA synthase in complex with ferredoxin
    • Protein or peptide: CO-methylating acetyl-CoA synthase
    • Protein or peptide: Carbon monoxide dehydrogenase/acetyl-CoA synthase beta subunit
    • Protein or peptide: Ferredoxin
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: Fe(3)-Ni(1)-S(4) cluster

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Supramolecule #1: Carbon monoxide dehydrogenase/acetyl-CoA synthase in complex with...

SupramoleculeName: Carbon monoxide dehydrogenase/acetyl-CoA synthase in complex with ferredoxin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Clostridium autoethanogenum DSM 10061 (bacteria)

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Macromolecule #1: CO-methylating acetyl-CoA synthase

MacromoleculeName: CO-methylating acetyl-CoA synthase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: CO-methylating acetyl-CoA synthase
Source (natural)Organism: Clostridium autoethanogenum DSM 10061 (bacteria)
Molecular weightTheoretical: 76.99107 KDa
SequenceString: MNLFQTVFTG SKQALAAAEG IVKQAVDEKG RDYKVAFPDT AYSLPVIFAA TGKKITNVGE LEGALDIVRS LIVEEEMLDK LLNSGLATA VAAEIIEAAK YVLSDAPYAE PCVGFISDPI IRSLGVPLVT GDIPGVAVIL GECPDSETAA KIIKDYQSKG L LTCLVGKV ...String:
MNLFQTVFTG SKQALAAAEG IVKQAVDEKG RDYKVAFPDT AYSLPVIFAA TGKKITNVGE LEGALDIVRS LIVEEEMLDK LLNSGLATA VAAEIIEAAK YVLSDAPYAE PCVGFISDPI IRSLGVPLVT GDIPGVAVIL GECPDSETAA KIIKDYQSKG L LTCLVGKV IDQAIEGKVK MGLDLRVIPL GYDVTSVIHV VTIAIRAALI FGGIKGGQLN DILKYTAERV PAFVNAFGPL SE LVVSAGA GAIALGFPVL TDQVVPEVPT LLLTQKDYDK MVKTSLEARN IKIKITEIPI PVSFAAAFEG ERIRKNDMLA EFG GNKTKA WELVMCADQG EVEDHKIEVI GPDIDTIDKA PGRMPLGMLI KVSGTNMQKD FEPVLERRLH YFLNYIEGVM HVGQ RNLTW VRIGKEAFEK GFRLKHFGEV IYAKMLDEFG SVVDKCEVTI ITDPGKAEEL EGKYAVPRYK ERDARLESLV DEKVD TFYS CNLCQSFAPA HVCIVTPERL GLCGAVSWLD AKATLELNPT GPCQAVPKEG VVDENLGIWE KVNETVSKIS QGAVTS VTL YSILQDPMTS CGCFECITGI MPEANGVVMV NREFGATTPL GMTFGELASM TGGGVQTPGF MGHGRQFIAS KKFMKGE GG LGRIVWMPKE LKDFVAEKLN KTAKELYNID NFADMICDET IATESEEVVK FLEEKGHPAL KMDPIM

UniProtKB: CO-methylating acetyl-CoA synthase

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Macromolecule #2: Carbon monoxide dehydrogenase/acetyl-CoA synthase beta subunit

MacromoleculeName: Carbon monoxide dehydrogenase/acetyl-CoA synthase beta subunit
type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: anaerobic carbon monoxide dehydrogenase
Source (natural)Organism: Clostridium autoethanogenum DSM 10061 (bacteria)
Molecular weightTheoretical: 67.846336 KDa
SequenceString: EEKAKSIDQA TLQLLDKAKQ DGVETVWDRK ADMKVQCGFG SAGVCCRNCS MGPCRVSPVP GKGVERGICG ATADVIVSRN FARMVAAGT AAHSDHGRSI ALSLYHTSKD GDIKVKDENK LKEVAKSFNV ETEGRDIYDI AHDVAKEGLS NYGKQLGEVT L PPSLPEKR ...String:
EEKAKSIDQA TLQLLDKAKQ DGVETVWDRK ADMKVQCGFG SAGVCCRNCS MGPCRVSPVP GKGVERGICG ATADVIVSRN FARMVAAGT AAHSDHGRSI ALSLYHTSKD GDIKVKDENK LKEVAKSFNV ETEGRDIYDI AHDVAKEGLS NYGKQLGEVT L PPSLPEKR KELWRKLGVY PRAVDREIAA VMHSTHIGCN ADAEAMIKMS MRCSLTDGWM GSFMGTEFSD IMFGTPHSID TE ANLGVLE KNSVNVVLHG HEPLLSEMVV EAASDPELVE LAKSVGADGI NLCGMCCTGN EVSMRHGIKI AGNFMQQELA VVT GAVDGL IVDVQCIMPA LAKLSKSYHT KFITTSPKAH ITDSIYMEFD EENPLDSAKK ILKEAILNFK NRDQSKVMIP ELKC KAILG YSVEEIINKL DKVVNTQIGP MQTVKPLADV LVSGVLRGAA AVVGCNNPKV VQDSAHIETI KGLIKNDVIV VVTGC AAQA AAKYGLLQKE AAEKYAGPGL ATVCKLVDIP PVLHMGSCVD ISRILDLVGR VANLLGVDMS DLPVAGVAPE WMSEKA VAI GTYVVTSGID TWLGVAPPVT GGPEVVDILT NKMEDWVGAK FFIETDPHKA VEQIVNRMNE KRKKLGI

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Macromolecule #3: Ferredoxin

MacromoleculeName: Ferredoxin / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Clostridium autoethanogenum DSM 10061 (bacteria)
Molecular weightTheoretical: 5.877546 KDa
SequenceString:
MAYKITEDCV SCGSCASECP ADAISQGDSQ FVIDPEKCIE CGNCANVCPV GAPVEES

UniProtKB: Ferredoxin

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Macromolecule #4: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 4 / Number of copies: 5 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #5: Fe(3)-Ni(1)-S(4) cluster

MacromoleculeName: Fe(3)-Ni(1)-S(4) cluster / type: ligand / ID: 5 / Number of copies: 2 / Formula: RQM
Molecular weightTheoretical: 410.333 Da
Chemical component information

ChemComp-RQM:
Fe(3)-Ni(1)-S(4) cluster

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 165000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 896132
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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